Sequence
atgc intronic sequence ATGC exonic sequencegtaattagcatacaaactaaatgtattatcagtattctcatctatggctgctgtaagcttgaagtgtgttcctgatttttgtttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
-------------------------------------------gtaattagcatacaaactaaatgtattatcagtattctcatctatggctgctgtaagcttgaagtgtgttcctgatttttgtttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA
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gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgtt-ctatcatat-tttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------------------------------------gtaattagcatacaaactaaatgtattatcagtattctcatctatggctgctgtaagcttga--agtgtgttcctgat----ttttgtttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA
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gtttgtacagaacctaccatggttctcactcataataatatgtgcttttcctccccatttttattaaggtttctgtgttgaaccactaaatgctcaaagtactgttttccccctcttttttctactcaactaatctaattcttatatacttttaaacgatcccagCGTGTACTTGATGCATTGTTCCCCTCAGTTCTTGGAGGAACATGTGCCATTCCTGGAGCTTTTGGTTGTGGAAAGACTGTCATTAGTCAGGCACTTTCCA
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 6
----------------------------------------------gtaattagcatacaaactaa--atgtattatcag----tattctcatctatg--gctgctgtaagcttgaagtgtgttcctgatttttgtttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA
| || | || | | | ||| |||| | || | | ||| || | ||| | | || || ||| | | ||||||||| || ||||| || ||||| || ||||| || || |||||||| || || ||||||||||||||||| ||||| ||||| ||||| || ||||| |
gtttgtctataagttgccttagcttggttgtctataattgtcagtttttgctaaaacttgaaatcgccaagcattttcagacgatgtttccctttatcttactccattaaatcttgaa-gtcttgtatgctttcaaatggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 9
gtaattagcatacaaactaaatgtattatcagtattctcatctatggct--gctgta--agcttgaagtgtgttcctgatttttgtttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA
||||| | | | |||||| ||||||| || ||| ||||| | || || ||| || || || | |||||||||||||||||||||||||| || ||||| || || ||||||||||||||||| || ||||||||||| ||||| ||||| ||||| ||||||||||
-----------gtaaactcagt-tgttatcaagtgtctcatccataatctaattgtgatagctttca-tgcgtaa-tgacttctgcttt-ttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATACCTGGAGCTTTTGGTTGTGGTAAAACTGTCATTAGTCAGGCTCTTTCTA
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 9
gtaattagcatacaaactaaatgtattatcagtattctcatctatg-----gctgctgtaagcttgaagtgtgttcctgatttttgtttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA
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-----------gtaaactcagt-tgttaccaagtgtctcctccatgatctaattgtgatagccttcatgc---ttaatgacttctgtttt-ttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATTCCTGGTGCTTTTGGTTGTGGTAAAACAGTCATTAGTCAGGCTCTTTCTA
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaattagcatacaaactaaatgtattatcagtattctcatctatggctgctgtaagcttgaagtgtgttcctgatttttgtttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA
|| |||| | || | || | || |||| | ||| ||| | || | || |||| |||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||| || ||||| ||||| ||||| || |||||||| || ||||| |
gtgattactcgattaattcttcttacagtggtgatagtcatttgaataca-tgtg---ttgctgattgctttcttttcctgttg----tcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
-gtaattagcatacaaactaaatgtattatcagtattctcatctatggctgctgtaagcttgaagtgtgttcc------tgatttttgtttcatct-cagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA
|| | | | || | |||| | | || | | || || | | |||| | ||| ||||| |||| | | | |||||| | || ||||| || |||||||||||||| || || ||||| ||||| ||||| |||||||| |||||||| || ||||| |||||||| || ||||
ggtttcaaattcatgactgaagtatatttatatgttacttacatgtgtgctgtgaatatctcaagtattttctctttgttgattgttgtcccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 9
---gtaattagcatacaaactaaatgtattatcagtattctcatctatggctgctgtaagcttgaagtg---tgttcctgattt---ttgtttcatct-cagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA
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tgtgttgggaatccatgaaccgattatgttttcgtgctttttatattgcactgcc--aacgttaaattcctttgcttctattttgaattgccccttttgcagCGAATACTGGATGCTCTGTTTCCGTCTGTCCTTGGAGGTACCTGCGCCATTCCTGGTGCATTTGGTTGTGGGAAGACCGTCATCAGTCAAGCACTTTCTAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|110692053|gb|EE070859.1|EE070859EST: GGCCTGTTGCATCAAAGCTGGCTGCTGATACCCCACTACTTACAGGACAG CGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATA
genomic: GGCCTGTTGCGTCAAAGCTGGCTGCTGATACCCCACTACTTACAGGACAGgtaattagca ... ttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatctatggctgctgtaagcttgaagtgtgttcctgatttttgtttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA
tcctgat putative branch site (score: 3)
tttttgtttcatctc CT-rich tract
atttttgttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattagcatacaaactaaatgtattatcagtattctcatctatggctgctgtaagcttgaagtgtgttcctgatttttgtttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT